How to use the pyensembl.ensembl_release.EnsemblRelease function in pyensembl

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github openvax / pyensembl / pyensembl / ensembl_release.py View on Github external
def __eq__(self, other):
        return (
            other.__class__ is EnsemblRelease and
            self.release == other.release and
            self.species == other.species)
github openvax / pyensembl / pyensembl / shell.py View on Github external
def all_combinations_of_ensembl_genomes(args):
    """
    Use all combinations of species and release versions specified by the
    commandline arguments to return a list of EnsemblRelease or Genome objects.
    The results will typically be of type EnsemblRelease unless the
    --custom-mirror argument was given.
    """
    species_list = args.species if args.species else ["human"]
    release_list = args.release if args.release else [MAX_ENSEMBL_RELEASE]
    genomes = []
    for species in species_list:
        # Otherwise, use Ensembl release information
        for version in release_list:
            ensembl_release = EnsemblRelease(version, species=species)

            if not args.custom_mirror:
                genomes.append(ensembl_release)
            else:
                # if we're using a custom mirror then we expect the provided
                # URL to be a directory with all the same filenames as
                # would be provided by Ensembl
                gtf_url = os.path.join(
                    args.custom_mirror,
                    os.path.basename(ensembl_release.gtf_url))
                transcript_fasta_urls = [
                    os.path.join(
                        args.custom_mirror,
                        os.path.basename(transcript_fasta_url))
                    for transcript_fasta_url in ensembl_release.transcript_fasta_urls
                ]
github openvax / pyensembl / pyensembl / shell.py View on Github external
def collect_all_installed_ensembl_releases():
    genomes = []
    for (species, release) in Species.all_species_release_pairs():
        genome = EnsemblRelease(release, species=species)
        if genome.required_local_files_exist():
            genomes.append(genome)
    return sorted(genomes, key=lambda g: (g.species.latin_name, g.release))